Quite simply: the closer a food is to it's natural state, the better it is for you. The more it has been processed, the worse it is for you.
Chemicals that are not naturally consumed in large amounts, such as chlorine and flouride in tap water, are not good for you.
Being healthy consists of much more that just 'calorie intake and burning calories'. Nutrients, vitamins, minerals, enzymes, chemicals, charged particles, etc. all play a part in your health. It seems 'common sense' to me that natural foods are going to be better than processed foods. Humans survived for thousands of years off of the foods that grew naturally on this Earth. If time travel were possible, going back 100 years and going into a grocery store would look MUCH different than it does today, and it would be healthier.
Anyway, arguing is pointless. Most people are too closed-minded and mentally influenced from birth in this country (read: brainwashed) to believe anything but the FDA and drug companies. Nevermind that drug companies do the EXACT same thing as Mercola... tell you about a 'problem' and then sell you their drug to 'fix it'.
Oh yeah, natural supplements almost never have any side effects. How many synthetic drugs have zero side effects? Zero.